Type in the masses you want to decompose. If you have more
than one mass, leave a space in between. Example:

2053.3 2247.5 4525.7

If multiple masses are given, each of them is decomposed
separately.

Please note: When using an amino acid alphabet, only masses
up to approximately 1600 Da can be decomposed in
reasonable time! (Using an allowed mass
error of 0.1 Da. Using a lower mass error, larger
masses can be decomposed). If the computation takes too long
(> 1 Minute), it will be cancelled.

Another possibility to provide input masses is by
uploading a
file from your computer. The following table shows
which file formats are supported and which file extensions are
used to recognize them.

Format

File extensions

Sequest

.dta, .DTA

Micromass

.pkl, .PKL

Mascot Generic Format

.mgf, .MGF

mzData

.mzData, .mzdata, .MZDATA, .xml

mzXML

.mzXML, .mzxml, .MZXML

Plain Text

.txt

Text as comma-separated values

.csv, .CSV

The next option lets you select whether your input molecules
have a monoisotopic or average isotopic mass
distribution. This does not influence how your input masses are
interpreted, but changes which alphabet is chosen and also how
modifications are calculated.

The allowed mass
error gives a tolerance for the mass of the resulting
decompositions. If, for example, your input mass is
2053.3 Da and the allowed mass error is set to 0.1 Da
(absolute), then all decompositions with mass at least
2053.2 Da and at most 2053.4 Da will be computed. If
any of the filtering options are enabled,
not all of them will be output, however.

The last option in this area is the computational precision, which
determines how Decomp rounds real-valued masses to integers.
This is necessary since the decomposition algorithm that Decomp
uses works for integers. For example, if an input or alphabet
mass is 1362.3418 Da, while the precision is set to
0.01 Da, then the resulting integer mass will be 136234.
Because Decomp determines this setting automatically, you
usually do not have to worry about it.

For each of the three predefined alphabets, one version
with a monoisotopic and one version with an average isotopic
mass distribution exist. Which alphabet is chosen depends on
the setting for the mass distribution. If Javascript is enabled
and a predefined alphabet is selected, the correct alphabet is
shown in the input field for custom alphabets. To input a
custom alphabet based on this predefined alphabet, simply
modify it in the text field.

Nucleotides

The nucleotide alphabet consists of the four nucleotides
Adenine, Cytosine, Guanine, and Thymine.

Amino Acids

The amino acid alphabet consists of 19 amino acids.
Isoleucin, which has the same mass as leucin, is not
included.

Atoms

The atom alphabet consists of the six elements Hydrogen,
Carbon, Nitrogen, Oxygen, Phosporus, and Sulfur.

Custom Alphabets

When JavaScript is enabled, look at the input field for
custom alphabets. When writing your own custom alphabet,
follow the given schema. More precisely, an alphabet is a text
file in which an alphabet character is defined in each line
like this:name mass
The name may be any sequence of letters, digits, and symbols,
but it should not start or end with a digit. If it does, you
will not get an error message, but you may get problems reading
the results. The mass must be a positive real number, possibly
in scientific notation. For example, 23,
42.89, 1e-5 and 2.3e7 are valid, but
-7.3 and 0.0 are not. Name and mass must be separated
by space or tab. If a line starts with a #, then the
line is interpreted as a comment and ignored. Empty lines are
also ignored.

If you want to upload an alphabet file, it must be
prepared following the same rules as above.

If you know some constraints about the molecules you want to
decompose, you can use this option to show only the relevant
results. For example, if you know, when decomposing DNA, that
there must be at least four Adenines, but at most six
Cytosines, type A4 into the text field next to
"Decomposition must contain at least" and type
C6 into the field next to "Decomposition must
contain at most". Multiple constraints can also be given,
separated by space.

If you want to use this, the names for your alphabet
characters can only contain the following characters:

Three types of modifications can be used. First, mass
modifications concerning the entire molecule, then, for
the amino acid alphabet, fixed and variable
modifications. In the two latter selectors, multiple
selections are allowed, just hold down the Ctrl key
while clicking on an item to select or deselect it.

Modifications of the Entire Molecule

Select a modification of the entire molecule here. The
effect is that, before decomposition, the modification is
'undone' by either subtracting or adding the appropriate mass
to or from the input mass.

Fixed Modifications

If a fixed modification is selected, it is assumed
that all amino acids of the given type have been
modified. For example, if "Acetylation (M, +42 Da)" has
been selected, then the decomposition algorithm will assume
that all Methionines (M) have been acetylated. Internally, this
is accomplished by changing the alphabet such that the mass of
a Methionine is increased by 42 Da.

Variable Modifications

If a variable modification is selected, it is
assumed that some amino acids of the given type have
been modified. This includes the special cases that none or all
have been modified. For example, if "Methylation (H,
+14 Da)" has been selected, then the decomposition
algorithm will assume that all Histidines occurring in the
decomposition may be methylated or not. Internally, this is
accomplished by adding another Histidine (called H')
to the alphabet that has a mass which is 14 Da greater
than the mass of the regular Histidine. In the output, regular
and modified versions can be distinguished since modified
Histidines have a ' symbol appended whereas regular
ones appear normally.

If this option is selected, a variant of the SENIOR rule is
used to filter out those decompositions that are chemically
implausible.

Let S be the the sum of valences of all atoms in
the decomposition and n be the number of atoms. The
two conditions are (from Kind and Fiehn):

S must be even.

S≥ 2n-2

Decomp knows valences for all of the atoms in the predefined
alphabet (CHNOPS). In addition, it knows the valences of Na, K,
Cl, Si, Br, F, Mg, Fe, and I. All of these elements can
therefore be used in a custom alphabet while the check for
chemically plausible decompositions still works.

Show Actual Mass and Deviation from Query Mass

If the option Show
actual mass for each decomposition. is selected, Decomp
will include, for every decomposition, its actual mass. The
actual mass may be different from the query mass when the
allowed mass error is set to a value greater than zero.